...nearly 10 even with the insert of nodes one at a time.

Profiling shows that...

...you basically have is a "chain" of nodes, and each list simply references a part...

...ref semantics: Just shared owner ship of nodes...

EG:
--------
import std.stdio, std.container;

void...

...new list with head + list. Making the nodes garbage collected would save on memory usage.

...refers to a freed node. Maybe the nodes could be refcounted, though a downside there...

...list that contains both GC-allocated nodes and malloc() nodes. That's just a bomb...

...auto degreeRank(NodeT)(NodeT nodes)
    {
        size_t[] x;
        foreach(node; nodes)
            x ~= node.links.length...

...but
assert (nodes[root2.pg.pgNo] == root2.pg.pgNo);
should have read
assert (nodes[root2...

...but
assert (nodes[root2.pg.pgNo] == root2.pg.pgNo);
should have read
assert (nodes[root2...

...code will generate 100s of millions of nodes, and each node on average is used...